Confined water

Quasi-one-dimensional ice is a stack of prism blocks (Frame.find_prisms). Quasi-two-dimensional ice is a sheet of primitive rings (Frame.monolayer_rings) plus an in-plane radial distribution (Frame.rdf_2d). The seams CLI does not grow a command for the prisms or the sheet. seams rdf is the three-dimensional partial RDF, not the in-plane histogram.

The 2020 nanotube and monolayer dumps are figshare project 73545. They are not in this repository, and this page does not invent their counts.

The in-tree confined frame is input/traj/exampleTraj.lammpstrj. The runnable copy is docs/tutorials/test_confined.py. Install Python with pip install pydseamslib.

import pydseams as ds

frame = ds.read("input/traj/exampleTraj.lammpstrj", atom_type=2)
r, g = frame.rdf_2d("output", cutoff=6.0, binwidth=0.5)
frame.monolayer_rings("output", sheet_area=1.0, max_depth=6)
frame.find_prisms(output_dir="output", max_depth=4)

sheet_area is the area the coverage fraction divides by. Use the area of the sheet you loaded. The ring counts themselves do not use it.